The Senegal international appeared to elbow Everton defender Coleman in the 29th minute of Newcastle's 3-2 victory at St James' Park, although he was not punished at the time as referee Craig Pawson did not see the incident.
Everton boss Roberto Martinez slammed the referee's decision as "unacceptable", with the 29-year-old rubbing further salt in the wounds by scoring Newcastle's equaliser to add to the Spaniard's frustrations.
However, Cisse will face retrospective action after the Football Association (FA) opened disciplinary proceedings on Monday.
The striker has until 6pm on Tuesday to respond to the charge and faces the prospect of a three-match suspension if found guilty.
That would see Cisse miss Newcastle's Premier League games against Burnley and Chelsea, as well as the FA Cup third-round clash with Leicester City.
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